Staphylococcus aureus is a gram-positive bacteria known for its multidrug resistance and persistent survival. H2S increased drug resistance and persistent survival in S. aureus, which produces H2S through the PLP-dependent enzyme MccB. In this study, we investigated the catalytic activities of S. aureus MccB in H2S production and explored its inhibitory effects of natural compounds. We found that the natural compound EGCG strongly inhibited MccB enzyme activity in H2S production via an unexpected mechanism. The mass and NMR analysis revealed that EGCG formed a hemiacetal compound with free PLP, resulting in the depletion of the cytosolic pool of PLP. EGCG enhanced the antibiotic effect of antibiotics retarded by MccB. Our results shed light on a novel pathway through which EGCG regulates bacterial H2S production, and this finding may have potential applications in diets aimed at suppressing the pathogenesis of S. aureus in the gut using the edible compound EGCG.